Molecular quantitative trait loci

F Aguet, K Alasoo, YI Li, A Battle, HK Im… - Nature Reviews …, 2023 - nature.com
Understanding functional effects of genetic variants is one of the key challenges in human
genetics, as much of disease-associated variation is located in non-coding regions with …

3′ UTR heterogeneity and cancer progression

JJ Chan, H Tabatabaeian, Y Tay - Trends in Cell Biology, 2023 - cell.com
The majority of human mRNAs generate alternative 3′ untranslated regions (UTRs)
through various processes, including RNA modifications such as RNA editing, m 6 A …

Systematic differences in discovery of genetic effects on gene expression and complex traits

H Mostafavi, JP Spence, S Naqvi, JK Pritchard - Nature Genetics, 2023 - nature.com
Most signals in genome-wide association studies (GWAS) of complex traits implicate
noncoding genetic variants with putative gene regulatory effects. However, currently …

Long 3′ UTRs predispose neurons to inflammation by promoting immunostimulatory double-stranded RNA formation

TJ Dorrity, H Shin, KA Wiegand, J Aruda… - Science …, 2023 - science.org
Loss of RNA homeostasis underlies numerous neurodegenerative and neuroinflammatory
diseases. However, the molecular mechanisms that trigger neuroinflammation are poorly …

Limited overlap of eQTLs and GWAS hits due to systematic differences in discovery

H Mostafavi, JP Spence, S Naqvi, JK Pritchard - BioRxiv, 2022 - biorxiv.org
Most signals in genome-wide association studies (GWAS) of complex traits point to
noncoding genetic variants with putative gene regulatory effects. However, currently …

A compressed variance component mixed model for detecting QTNs and QTN-by-environment and QTN-by-QTN interactions in genome-wide association studies

M Li, YW Zhang, ZC Zhang, Y Xiang, MH Liu, YH Zhou… - Molecular Plant, 2022 - cell.com
Although genome-wide association studies are widely used to mine genes for quantitative
traits, the effects to be estimated are confounded, and the methodologies for detecting …

[HTML][HTML] Genome-wide functional screen of 3′ UTR variants uncovers causal variants for human disease and evolution

D Griesemer, JR Xue, SK Reilly, JC Ulirsch, K Kukreja… - Cell, 2021 - cell.com
Summary 3′ untranslated region (3′ UTR) variants are strongly associated with human
traits and diseases, yet few have been causally identified. We developed the massively …

Splicing QTL analysis focusing on coding sequences reveals mechanisms for disease susceptibility loci

K Yamaguchi, K Ishigaki, A Suzuki, Y Tsuchida… - Nature …, 2022 - nature.com
Splicing quantitative trait loci (sQTLs) are one of the major causal mechanisms in genome-
wide association study (GWAS) loci, but their role in disease pathogenesis is poorly …

Context-specific regulation and function of mRNA alternative polyadenylation

S Mitschka, C Mayr - Nature Reviews Molecular Cell Biology, 2022 - nature.com
Alternative cleavage and polyadenylation (APA) is a widespread mechanism to generate
mRNA isoforms with alternative 3′ untranslated regions (UTRs). The expression of …

Deep learning of human polyadenylation sites at nucleotide resolution reveals molecular determinants of site usage and relevance in disease

EK Stroup, Z Ji - Nature communications, 2023 - nature.com
The genomic distribution of cleavage and polyadenylation (polyA) sites should be co-
evolutionally optimized with the local gene structure. Otherwise, spurious polyadenylation …